In [3]:
import pandas as pd
import dash
from dash import dcc, html
from dash.dependencies import Input, Output
from rdkit import Chem
from rdkit.Chem import Draw
from pandas_profiling import ProfileReport

I - Data¶

OpenFoodTox is a structured database summarising the outcomes of hazard identification and characterisation for the human health (all regulated products and contaminants), the animal health (feed additives, pesticides and contaminants) and the environment (feed additives and pesticides).

OpenFoodTox provides information on the substance characterisation, the links to EFSA’s related output, background European legislation, and a summary of the critical toxicological endpoints and reference values.

a) Substance characterisation:¶

This is the database showing the chemical of each substances including CAS number and structure

In [4]:
SubCharacter = pd.read_csv('/Users/suongsuong/Documents/GitHub/Data400_Spring24/MiniProject/Data/SubstanceCharacterisation_KJ_2022.csv')
SubCharacter
Out[4]:
Substance has Component CASNumber ECRefNo MolecularFormula smiles
0 ((E)-2-(2-hydroxymethylphenyl)-2-methoxyimino-... as such ((E)-2-(2-hydroxymethylphenyl)-2-methoxyimino-... NaN NaN C11H14N2O3 OCc1ccccc1/C(=N\OC)C(=O)NC
1 ((E)-2-(2-hydroxymethylphenyl)-2-methoxyimino-... metabolite Dimoxystrobin 149961-52-4 NaN C19H22N2O3 CC1=CC(=C(C=C1)C)OCC2=CC=CC=C2C(=NOC)C(=O)NC
2 (+)-13alpha-Tigloyloxylupanine as such (+)-13-alpha-Tigloyloxylupanine 57943-34-7 NaN C20H30N2O3 CC=C(C)C(=O)OC1CCN2CC3CC(C2C1)CN4C3CCCC4=O
3 (+)-13alpha-hydroxy-lupanine as such (+)-13-Alpha-hydroxy-lupanine 15358-48-2 NaN C15H24N2O2 C1CC2C3CC(CN2C(=O)C1)C4CC(CCN4C3)O
4 (+)-Alpha-cedrene as such (+)-Alpha-cedrene 35964-52-4 NaN C15H24 CC1=CCC23C[C@H]1C(C)(C)[C@H]3CC[C@@H]2C
... ... ... ... ... ... ... ...
7600 trans-3-Hexenyl formate as such trans-3-Hexenyl formate 56922-80-6 260-442-7 C7H12O2 CC\C=C\CCOC=O
7601 trans-3-Hexenyl hexanoate as such trans-3-Hexenyl hexanoate 56922-82-8 260-444-8 C12H22O2 CCCCCC(=O)OCC\C=C\CC
7602 trans-3-Methyl-2-(2-pentenyl)-2-cyclopenten-1-one as such trans-3-Methyl-2-(2-pentenyl)-2-cyclopenten-1-one 6261-18-3 228-410-7 C11H16O CC\C=C\CC1=C(C)CCC1=O
7603 trans-6-Methyl-3-hepten-2-one as such trans-6-Methyl-3-hepten-2-one 20859-10-3 NaN C8H14O CC(C)C/C=C/C(=O)C
7604 trans-Menthone as such trans-Menthone 89-80-5 201-941-1 C10H18O CC(C)[C@H]1CC[C@H](C)CC1=O

7605 rows × 7 columns

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b) Reference value:¶

Reference Value : The estimated maximum dose (on a body mass basis) or the concentration of an agent to which an individual may be exposed over a specified period without appreciable risk. R

In [5]:
ref_value = pd.read_csv('/Users/suongsuong/Documents/GitHub/Data400_Spring24/MiniProject/Data/ReferenceValues_KJ_2022.csv')
RefValue = ref_value.drop(columns=['Author','Year','qualfier','Assessment'])
RefValue
Out[5]:
Substance OutputID value unit Population
0 (-)-3,7-Dimethyl-6-octen-1-ol 2180 30.0 µg/kg bw/day Consumers
1 (-)-3,7-Dimethyl-6-octen-1-ol 2864 4.4 mg/kg Cats as pet
2 (-)-3,7-Dimethyl-6-octen-1-ol 2864 8.0 mg/kg Chicken for egg production
3 (-)-3,7-Dimethyl-6-octen-1-ol 2864 8.0 mg/kg Chicken for meat production
4 (-)-3,7-Dimethyl-6-octen-1-ol 2864 10.0 mg/kg Pigs - less than 1 year old
... ... ... ... ... ...
11052 trans-Menthone 2822 0.3 mg/kg Pigs
11053 trans-Menthone 2822 0.3 mg/kg Poultry
11054 trans-Menthone 2822 0.5 mg/kg Animal not used for food production - unspecified
11055 trans-Menthone 2822 0.5 mg/kg Cattle
11056 trans-Menthone 2822 0.5 mg/kg Salmons

11057 rows × 5 columns

c) Reference point:¶

A reference point is like a starting point scientists use when they're figuring out how much of a substance can be harmful.

In [6]:
RefPoint = pd.read_csv('/Users/suongsuong/Documents/GitHub/Data400_Spring24/MiniProject/Data/ReferencePoints_KJ_2022.csv')
#RefPoint = ref_point.drop(columns=['Substance','Author','Year','qualifier'])
RefPoint
Out[6]:
Substance Author Year OutputID Study TestType Species Route DurationDays Endpoint qualifier value unit Effect Toxicity
0 (-)-3,7-Dimethyl-6-octen-1-ol EFSA FEEDAP 2016 2864 Animal (target species) health subchronic Rat oral: feed 84.0 NOEL = 50.000 mg/kg bw/day no adverse effect observed NaN
1 (-)-Hyoscyamine and (-)-Scopolamine group EFSA CONTAM 2013 2396 Animal (target species) health not reported Pig Not reported NaN NOAEL = 1500.000 µg/kg not reported not reported
2 (-)-Hyoscyamine and (-)-Scopolamine group EFSA CONTAM 2013 2396 Human health study with volunteers Human Not reported NaN NOAEL = 0.160 µg/kg bw clinical signs systemic
3 (1R,2S,5R)-N-(2-(Pyridine-2-yl)ethyl)-3-p-ment... EFSA CEF 2014 2524 Human health subchronic Rat oral: feed 90.0 NOAEL = 5.000 mg/kg bw/day histopathology non neoplastic endocrine
4 (1R,2S,5R)-N-(4-Methoxyphenyl)-5-methyl-2-(1-m... EFSA CEF 2012 2147 Human health subchronic Rat oral: feed 90.0 NOAEL = 100.000 mg/kg bw/day organ weights hepatotoxicity
... ... ... ... ... ... ... ... ... ... ... ... ... ... ... ...
13349 p-Mentha-1,8-dien-7-ol EFSA CEF 2012 2130 Human health subchronic Rat oral: gavage 90.0 dose level = 120.000 mg/kg bw/day no adverse effect observed NaN
13350 p-Mentha-1,8-dien-7-ol EFSA CEF 2013 2376 Human health subchronic Dog Not reported 90.0 dose level = 120.000 mg/kg bw no adverse effect observed NaN
13351 p-Mentha-1,8-dien-7-ol EFSA CEF 2013 2376 Human health subchronic Rat oral: gavage 90.0 dose level = 120.000 mg/kg bw/day no adverse effect observed NaN
13352 sec-Butan-3-onyl acetate EFSA FEEDAP 2016 2887 Animal (target species) health subchronic Rat oral: gavage 90.0 NOAEL = 90.000 mg/kg bw/day mortality systemic
13353 tr-1-(2,6,6-Trimethyl-1-cyclohexen-1-yl)but-2-... EFSA FEEDAP 2016 2822 Ecotox (water compartment) acute toxicity Green alga Not reported NaN EC50 = 0.828 mg/L mortality NaN

13354 rows × 15 columns

d) Genetoxicity:¶

Genotoxicity is the property of chemical agents that damage the genetic information within a cell causing mutations, which may lead to cancer

In [7]:
GenTox = pd.read_csv('/Users/suongsuong/Documents/GitHub/Data400_Spring24/MiniProject/Data/Genotoxicity_KJ_2022.csv')
#GenTox = Gen_tox.drop(columns=['Substance','Author','Year'])
GenTox
Out[7]:
Substance Author Year OutputID Genotoxicity
0 ((E)-2-(2-hydroxymethylphenyl)-2-methoxyimino-... EFSA 2005 1060 Negative
1 (+)-13alpha-Tigloyloxylupanine EFSA CONTAM 2019 3321 Negative
2 (+)-13alpha-hydroxy-lupanine EFSA CONTAM 2019 3321 Negative
3 (+)-Alpha-cedrene EFSA AFC 2008 2299 Not determined
4 (+)-Alpha-cedrene EFSA CEF 2010 2039 Not determined
... ... ... ... ... ...
10506 trans-3-Methyl-2-(2-pentenyl)-2-cyclopenten-1-one EFSA CEF 2015 2654 Negative
10507 trans-3-Methyl-2-(2-pentenyl)-2-cyclopenten-1-one EFSA CEF 2015 2693 Negative
10508 trans-6-Methyl-3-hepten-2-one EFSA CEF 2012 2165 Ambiguous
10509 trans-6-Methyl-3-hepten-2-one EFSA FAF 2019 3259 Negative
10510 trans-Menthone EFSA FEEDAP 2016 2822 Not determined

10511 rows × 5 columns

II - EDA¶

In [8]:
ProfileReport(SubCharacter, title='Subtance Characterization Data Report', explorative=True)

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ProfileReport(RefValue, title='Reference Value Data Report', explorative=True)



     






















    
    








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ProfileReport(RefPoint, title='Reference Point Data Report', explorative=True)



     






















    
    








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ProfileReport(GenTox, title='Genotoxicity Data Report', explorative=True)



     






















    
    








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In [12]:



     


SubCharacter.dropna(inplace=True)
RefValue.dropna(inplace=True)
RefValue.drop_duplicates(inplace=True)
RefPoint.dropna(inplace=True)
GenTox.dropna(inplace=True)



     



















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GenTox.shape



     






















    
    
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(10511, 5)
























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III - Interactive Dashboard¶
This part is not completed yet, the interface could be later improved























http://127.0.0.1:8050/



















In [14]:



     


# Initialize Dash app
app = dash.Dash(__name__)

# Define layout
app.layout = html.Div([
    html.H1("Substance Information Dashboard", style={'textAlign': 'center', 'color': '#0074D9', 'marginBottom': '20px'}),
    dcc.Input(id='substance-input', type='text', placeholder='Enter substance...', style={'width': '50%', 'margin': 'auto', 'textAlign': 'center'}),
    html.Div(id='output-container', style={'margin': '20px'})
], style={'fontFamily': 'Arial, sans-serif', 'maxWidth': '800px', 'margin': 'auto'})

# Define callback to update output
@app.callback(
    Output('output-container', 'children'),
    [Input('substance-input', 'value')]
)
def update_output(substance_input):
    if substance_input is not None:
        # Molecule
        smiles = SubCharacter[SubCharacter['Substance'] == substance_input]['smiles'].values[0]
        mol = Chem.MolFromSmiles(smiles)
        img = Draw.MolToImage(mol, size=(300, 300))
        Return_Structure = html.Div([
            html.H3("Chemical Structure:"),
            html.Div([html.Img(src=img, style={'display': 'block', 'margin': 'auto'})])
        ])
        
        # RefValue
        selected_substance_refvalue = RefValue[RefValue['Substance'] == substance_input]
        if not selected_substance_refvalue.empty:
            refvalue = selected_substance_refvalue['value'].values[0]
            refunit = selected_substance_refvalue['unit'].values[0]
            Return_RefValue = html.Div([
                html.H3("Reference Value", style={'color': '#2ECC40'}),
                html.P("A reference value is like a safety limit for how much of a substance someone can be exposed to without significant risk.", style={'marginBottom': '10px'}),
                html.P(f"The reference value for {substance_input} is {refvalue} {refunit}", style={'fontWeight': 'bold'})
            ])
        else:
            Return_RefValue = html.Div("Reference Value not found", style={'color': '#FF4136'})
        
        # RefPoint
        selected_substance_refpoint = RefPoint[RefPoint['Substance'] == substance_input]
        if not selected_substance_refpoint.empty:
            pointvalue = selected_substance_refpoint['value'].values[0]
            pointunit = selected_substance_refpoint['unit'].values[0]
            Return_RefPoint = html.Div([
                html.H3("Reference Point", style={'color': '#2ECC40'}),
                html.P("A reference point is like a starting point scientists use when they're figuring out how much of a substance can be harmful.", style={'marginBottom': '10px'}),
                html.P(f"The reference point for {substance_input} is {pointvalue} {pointunit}", style={'fontWeight': 'bold'})
            ])
        else:
            Return_RefPoint = html.Div("Reference Point not found", style={'color': '#FF4136'})        
        
        # Gentoxicity 
        selected_substance_gentox = GenTox[GenTox['Substance'] == substance_input]
        if not selected_substance_gentox.empty:
            gentox = selected_substance_gentox['Genotoxicity'].values[0]
            Return_gentox = html.Div([
                html.H3("Genotoxicity", style={'color': '#2ECC40'}),
                html.P("Genotoxicity is the property of chemical agents that damage the genetic information within a cell causing mutations, which may lead to cancer.", style={'marginBottom': '10px'}),
                html.P(f"Genotoxicity for {substance_input} is {gentox}", style={'fontWeight': 'bold'})
            ])
        else:
            Return_gentox = html.Div("Genotoxicity not found", style={'color': '#FF4136'})        
        
        return [
            Return_Structure,
            Return_RefValue,
            Return_RefPoint,
            Return_gentox
        ]
    else:
        return html.Div("Substance not found", style={'color': '#FF4136', 'fontWeight': 'bold', 'textAlign': 'center'})

if __name__ == '__main__':
    app.run_server(debug=True)



     






















    
    







        
        























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